Vaginal microbiome and serum metabolite differences in late gestation commercial sows at risk for pelvic organ prolapse

Combined analysis of 16S rRNA gene sequencing data reveals core vaginal bacteria across livestock species

Investigating the livestock vaginal microbiota is of increasing interest due to its relationship with animal reproductive performance. Recent publications have uncovered a high degree of variability of the livestock vaginal microbiota, making it difficult to focus functional research on individual microorganisms. To address this variability, we conducted a combined analysis of publicly available 16S rRNA gene amplicon sequencing datasets to reveal the core vaginal microbiota in cattle, sheep, and pigs. The goal of this combined analysis was to identify bacterial genera that were shared despite a diverse overall sample population. A total of 2,911 vaginal samples (715 cattle, 964 sheep, and 1,232 pigs) from 29 different datasets were used in this combined analysis. Beta diversity analysis revealed structural differences of the vaginal microbiota between different animal species. Compositionally, the most abundant phyla were Bacillota, Pseudomonadota, and Bacteroidota. At the genus level, an unclassified Pasteurellaceae genus, Ureaplasma, and Streptococcus were the most abundant. Across the vaginal microbiota of individual livestock species, compositional differences were observed. The cattle and sheep vaginal microbiota contained a higher abundance of Ureaplasma and Histophilus whereas the pig vaginal microbiota contained more Fusobacterium and Parvimonas than that of the other livestock samples. Among the cattle, 120 OTUs and 82 genera were present in 70% of the vaginal samples. At the same threshold, pig samples had 40 core OTUs and 63 core genera, while the sheep samples had 22 core OTUs and 50 core genera. There were 19 overlapping core vaginal genera across the three animal species. The core vaginal OTUs were largely species-specific, although there were eight overlapping OTUs. These included Streptococcus (OTU 21), Clostridium sensu stricto 1 (OTU 18), and Corynebacterium (OTU 6), which were also some of the most abundant members of the livestock core vaginal microbiota. A better understanding of the livestock vaginal microbiota is required for future studies aimed at elucidation of the functional significance of individual microbes with respect to livestock reproductive efficiency. The core vaginal genera identified in this analysis will help guide research on mechanisms/pathways through which individual organisms enhance or impede animal reproductive efficiency.

Too late or too soon? The replacement gilt paradox

Due to high annual culling rates, pig farms require a constant income of replacement gilts. Gilts typically reach puberty at nearly six months of age. Puberty may be induced through early boar exposure, therapy with steroid hormones and chorionic gonadotropins, and optimized by identifying biological predictors and risk factors. Old age at the time of the first mating is associated with an increased risk of premature culling, often attributed to reproductive failures and locomotor problems. While female prolifacy has increased substantially during the last few decades, selecting for litter size to optimize lifetime productivity would be more efficient after two parities. Additionally, uterine capacity and the number of functional teats should be considered in selecting future dams. For each female, the cost-effective number of parities at removal is determined by the cumulative number of pigs born and weaned during the total herd days.

Evaluation of fecal microbiota of late gestation sows in relation to pelvic organ prolapse risk

Introduction

Sow mortality in the U.S. swine industry has increased in recent years, for which pelvic organ prolapse (POP) is a major contributor, accounting for 21% of all sow mortality. Dysbiosis of microbial communities has been associated with disease and reproductive dysfunction in several species, and previous studies have shown changes in vaginal microbiota in sows with increased risk for POP during late gestation. However, there is insufficient knowledge surrounding the potential relationship between fecal microbiota and POP in sows. Therefore, the study objective was to identify differences in sow fecal microbiota and determine if fecal and vaginal microbial communities are correlated in relation to POP risk.

Methods

Sows were evaluated for POP risk using an established perineal scoring system, with a perineal score (PS) of 1 (PS1) presuming little to no risk of POP to a PS of 3 (PS3) presuming high risk of POP. In the current study, 2,864 sows were scored during gestation week 15, and 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Fecal swabs (n = 215) were collected between gestation days 108-115, DNA was extracted, and 16S rRNA gene amplicon sequencing libraries were analyzed using mothur, phyloseq and SAS in reference to PS and POP outcome. Additionally, co-occurrence networks were constructed using CoNet to compare fecal and vaginal microbiota from the same cohort of sows and identify correlations between different taxa.

Results

Differences in fecal community composition (PERMANOVA; P < 0.05), structure (alpha diversity measurements; P < 0.05), and 13 individual operational taxonomic units (OTUs) were revealed between PS1 and PS3 assigned sows. No differences in fecal microbiota were detected as a result of POP outcome. However, the abundances of several taxa were correlated across sample collection sites, suggesting the fecal and vaginal microbial communities may be related to one another.

Discussion

Collectively, fewer differences in the fecal microbiota exist in sows with differing risk for POP compared to the vaginal microbiota, suggesting the vaginal microbiome may be more relevant in relation to POP outcome, although correlations between fecal and vaginal communities may provide insight for strategies to combat POP.

Benefits of maternal pectin supplementation in gestation diet on vaginal microbiota of sows and intestinal health of newborn piglets

Pectin is a proven prebiotic and widely used in human health products. This study aims to assess the impact of dietary pectin supplementation during gestation on sow vaginal microbiota and the offspring's intestinal composition. Thirty sows were randomly allocated to two groups and fed a standard diet (CON) or a standard diet supplemented with 3 g/kg pectin (PEC). Blood, feces, and vaginal swab samples from the sows and blood, intestines issue, and colonic content samples from the offspring were collected and analyzed. The results indicate that the relative abundance of vaginal Lactobacillus was notably enhanced in the PEC group and fecal β-glucuronidase (β-G) activity and plasma 17β-estradiol (E2) concentration were also significantly increased in the PEC group. Newborn piglets were found to host different microbial communities as well. At the phylum level, Proteobacteria dominated in the CON group, and Firmicutes was predominant in the PEC group. Newborn piglets in the PEC group had a lower interleukin-6 (IL-6) concentration in their plasma. The expression of intestinal cytokines of offspring was improved as well. Villus height and villus height/crypt depth (V/C) in the PEC group were extremely higher than those in the CON group. In conclusion, dietary pectin supplementation can be of benefit to both sows and newborn piglets.

Managing Reproduction in Hyperprolific Sow Herds

The rearing of large litters from hyperprolific sows is a characteristic of modern genotypes. However, these sows have body and reproductive characteristics that differentiate them from the genotypes of the past decades, making it necessary to adopt different management strategies. This review describes the main care and challenges associated with the hyperprolificity of sows during the period in which replacement gilts are selected, along with gestation, parturition, lactation, and the weaning-estrus interval. It describes the challenges that these sows' piglets will face during the lactation period and includes some strategies adopted to develop these surplus piglets. In addition, it identifies areas where more research is needed to understand the reproductive management of modern genotypes.

Current practice in animal models for pelvic floor dysfunction

INTRODUCTION AND HYPOTHESIS

The objective was to explore the current practice of using animal models for female pelvic floor dysfunction (PFD).

METHODS

By applying PFD and animal models as the keywords, we made a computerized search using PubMed, Ovid-Medline and Ovid-Embase from 2000 to 2022. The publications on the construction and application of animal models for PFD were included, and the results are presented in narrative text.

RESULTS

Studies on PFD primarily use rodents, large quadrupeds, and nonhuman primates (NHPs). NHPs are closest to humans in anatomy and biomechanics of the pelvic floor, followed by large quadrupeds and rodents. Rodents are more suitable for studying molecular mechanism, histopathology of PFD, and mesh immune rejection. Large quadrupeds are adaptable to the study of pelvic floor biomechanics and the development of new surgical instruments for PFD. NHPs are suitable for studying the occurrence and pathogenesis of pelvic organ prolapse. Among modeling methods, violent destruction of pelvic floor muscles, regulation of hormone levels, and denervation were used to simulate the occurrence of PFD. Gene knockout can be used to study both the pathogenesis of PFD and the efficacy of treatments. Other methods such as abdominal wall defect, vaginal defect, and in vitro organ bath system are more frequently used to observe wound healing after surgery and to verify the efficacy of treatments.

CONCLUSIONS

The rat is currently the most applicable animal type for numerous modeling methods. Vaginal dilation is the most widely used modeling method for research on the pathogenesis, pathological changes, and treatment of PFD.

Identification of the genetic basis of sow pelvic organ prolapse

Introduction: Pelvic organ prolapse (POP) is one contributor to recent increases in sow mortality that have been observed in some populations and environments, leading to financial losses and welfare concerns. Methods: With inconsistent previous reports, the objective here was to investigate the role of genetics on susceptibility to POP, using data on 30,429 purebred sows, of which 14,186 were genotyped (25K), collected from 2012 to 2022 in two US multiplier farms with a high POP incidence of 7.1% among culled and dead sows and ranging from 2% to 4% of all sows present by parity. Given the low incidence of POP for parities 1 and >6, only data from parities 2 to 6 were retained for analyses. Genetic analyses were conducted both across parities, using cull data (culled for POP versus another reason), and by parity, using farrowing data. (culled for POP versus culled for another reason or not culled). Results and Discussion: Estimates of heritability from univariate logit models on the underlying scale were 0.35 ± 0.02 for the across-parity analysis and ranged from 0.41 ± 0.03 in parity 2 to 0.15 ± 0.07 in parity 6 for the by-parity analyses. Estimates of genetic correlations of POP between parities based on bivariate linear models indicated a similar genetic basis of POP across parities but less similar with increasing distance between parities. Genome wide association analyses revealed six 1 Mb windows that explained more than 1% of the genetic variance in the across-parity data. Most regions were confirmed in several by-parity analyses. Functional analyses of the identified genomic regions showed a potential role of several genes on chromosomes 1, 3, 7, 10, 12, and 14 in susceptibility to POP, including the Estrogen Receptor gene. Gene set enrichment analyses showed that genomic regions that explained more variation for POP were enriched for several terms from custom transcriptome and gene ontology libraries. Conclusion: The influence of genetics on susceptibility to POP in this population and environment was confirmed and several candidate genes and biological processes were identified that can be targeted to better understand and mitigate the incidence of POP.

Untargeted Metabolomics Pilot Study Using UHPLC-qTOF MS Profile in Sows' Urine Reveals Metabolites of Bladder Inflammation

Urinary tract infections (UTI) of sows (characterized by ascending infections of the urinary bladder (cyst), ureters, and renal pelvis), are major health issues with a significant economic impact to the swine industry. The current detection of UTI incidents lacks sensitivity; thus, UTIs remain largely under-diagnosed. The value of metabolomics in unraveling the mechanisms of sow UTI has not yet been established. This study aims to investigate the urine metabolome of sows for UTI biomarkers. Urine samples were collected from 58 culled sows from a farrow-to-finish herd in Greece. Urine metabolomic profiles in 31 healthy controls and in 27 inflammatory ones were evaluated. UHPLC-qTOF MS/MS was applied for the analysis with a combination of multivariate and univariate statistical analysis. Eighteen potential markers were found. The changes in several urine metabolites classes (nucleosides, indoles, isoflavones, and dipeptides), as well as amino-acids allowed for an adequate discrimination between the study groups. Identified metabolites were involved in purine metabolism; phenylalanine; tyrosine and tryptophan biosynthesis; and phenylalanine metabolism. Through ROC analysis it was shown that the 18 identified metabolite biomarkers exhibited good predictive accuracy. In summary, our study provided new information on the potential targets for predicting early and accurate diagnosis of UTI. Further, this information also sheds light on how it could be applied in live animals.

The sow microbiome: Current and future perspectives to maximize the productivity in swine herds

The development of new generation sequencing methods and the reduction in the cost per base sequenced over the past few years is drawing the attention of the pig industry to microbiome understanding and modulation. In recent years, there has been an increase in the number of articles published related to microbiome studies in swine. With respect to sows, microbiome studies mainly focused on the gut, with some studies evaluating the reproductive tract and mammary microbiome. However, studies about urinary microbiome are still lacking. The present literature indicates that the microbiome in the sow’s gut can affect the microbiome in other body parts. Moreover, the understanding of the dynamics and interactions among microbial populations within the sow or the herd has led to improvements in animal health and reproductive performance. This review provides new insights related to sow intestinal, urinary, mammary, and reproductive microbiomes and their relationships with reproductive outcomes, diseases, and early colonization in offspring by gathering the most recent work in this field as well as pinpoints information gaps that require further investigation. This literature review also sheds light on the knowledge regarding the role of microbiomes in the reduction of antimicrobial use.

Vaginal microbiota signatures in healthy and purulent vulvar discharge sows

Purulent vulvar discharges, primarily caused by genito-urinary tract infections, are an important source of economic loss for swine producers due to sow culling and mortality. However, the agents that compose the vaginal microbiota of sows and their changes during infections are not well understood. The first goal of this study was to characterize and compare the vaginal bacterial content of healthy (HE, n = 40) and purulent vulvar discharge sows (VD, n = 270) by a culture-dependent method and MALDI-TOF MS identification. Secondly, we performed 16S rRNA targeted metagenomic approach (n = 72) to compare the vaginal microbiota between these groups. We found a wide variety of bacteria, with Proteobacteria, Firmicutes, and Bacteroidota being the most abundant phyla in both groups, as well as Escherichia-Shigella, Streptococcus, and Bacteroides at the genus level. Most agents identified in the sequencing method also grew in the culture-dependent method, showing the viability of these bacteria. Alpha diversity did not differ between HE and VD sows, regarding sample richness and diversity, but a beta-diversity index showed a different microbiota composition between these groups in two tested herds. ANCOM analysis revealed that Bacteroides pyogenes were more abundant in VD females and can be a marker for this group. Other agents also require attention, such as the Streptococcus dysgalactiae and Staphylococcus hyicus found in remarkably greater relative abundance in VD sows. Network analysis revealed important positive correlations between some potentially pathogenic genera, such as between Escherichia-Shigella, Trueperella, Streptococcus, Corynebacterium, and Prevotella, which did not occur in healthy sows. We conclude that the alteration of the vaginal microbiota between healthy and purulent vulvar discharge sows, although not extreme, could be due to the increase in the relative abundance of specific agents and to associations between potentially pathogenic bacteria.

Vaginal microbiota differences associated with pelvic organ prolapse risk during late gestation in commercial sows

During the last decade, sow mortality due to pelvic organ prolapse (POP) has increased. To better understand the biology associated with POP, sows were phenotypically assessed and assigned a perineal score (PS) based on presumed POP risk and categorized as PS1 (low), PS2 (moderate), or PS3 (high). The study objective was to identify changes in sow vaginal microbiota that may be associated with POP. The hypothesis is that vaginal microbiota differs between sows with variable risk for POP, and changes in microbiota during late gestation exist between sows with differing risk. Of the 2864 sows scored during gestation week 15, 1.0, 2.7, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Vaginal swabs subjected to 16S rRNA gene sequencing revealed differences in community composition (Bray–Curtis; P < 0.05) and individual operational taxonomic unit (OTU) comparisons between vaginal microbiota of PS1 and PS3 sows at gestation week 15. Further, differences (P < 0.05) in community composition and OTUs (Q < 0.05) were observed in PS3 sows that either did or did not subsequently experience POP. Differences in community structure (alpha diversity measurements; P < 0.05), composition (P < 0.05), and OTUs (Q < 0.05) were observed in gestation week 12 sows scored PS1 compared to week 15 sows scored PS1 or PS3, suggesting that sow vaginal microbiota shifts during late gestation differently as POP risk changes. Collectively, these data demonstrate that sows with greater POP risk have unique vaginal microflora, for which a better understanding could aid in the development of mitigation strategies.

Circulating biomarkers associated with pelvic organ prolapse risk in late gestation sows

Sow mortality, as the result of pelvic organ prolapse (POP), has been increasing in the last decade in the U.S. swine industry. The objective of this study was to identify potential biological markers associated with risk of POP in sows. We hypothesized that sows differing in perineal score (PS) from PS1–PS3 (PS1—a presumed low POP risk; PS2—a presumed moderate POP risk; and PS3—a presumed high POP risk) would differ in circulatory biomarkers of inflammation and hormonal profiles. On gestation week 15, 2,864 individual sows were assigned a PS, and subsequently, 1.0%, 2.7%, and 23.4% of PS1, PS2, or PS3 sows, respectively, experienced POP. During PS assignment at days 107–116 of gestation, blood samples were collected from sows on two farms of similar genetics, feed sources, and health status. Whole blood was subjected to complete blood count (CBC) analysis (n = 212) and steroid hormones were measured in serum from a subset (n = 110) of animals assigned PS3 parity matched to PS1. Lipopolysaccharide-binding protein (LBP), tumor necrosis factor-alpha (TNF-α), haptoglobin, C-reactive protein (CRP), and creatine kinase (CK) levels were also evaluated. Complete blood count analysis revealed decreased (P ≤ 0.05) mean platelet volume (3.9%), lymphocytes (6.5%), and monocytes (7.5%) in PS3 compared to PS1 sows. Increased (P ≤ 0.02) abundance of androstenedione (13.4%), androsterone (18.2%), estrone (24.8%), and 17β-estradiol (26.2%) was observed in PS3 compared to PS1 sows. Additionally, a 25.8% increase (P = 0.04) in LBP in PS3 compared to PS1 sows was observed. Many dynamic physiological changes occur in sows during late gestation as they approach farrowing. The data presented herein demonstrate that distinct differences in concentrations of circulating biomarkers exist between late gestation sows at high or low risk for POP and may serve as a useful tool for understanding the etiology of POP and evaluation of mitigation strategies.

Vaginal bacterial diversity from healthy gilts and pregnant sows subjected to natural mating or artificial insemination

The profitability of commercial pig farms largely depends on the reproductive performance of gilts and sows. The aim of this study was to identify differences in the composition and diversity of vaginal microbiota between gilts (G) and pregnant (P) sows, both artificially inseminated (AI) and natural mating (NM). Samples were collected by scraping the vaginal mucosa of G (n = 10) and P (NM, n = 10 and AI, n = 7) sows. Samples were analysed by culture-dependent techniques and 16S-rRNA gene High-Throughput-Sequencing. The profiles of the cultured microbiota showed two distinctive clusters, one of them grouped four samples of P sows from the AI group. The vaginal microbiota from P had lower richness than G sows (Mann-Whitney/Kruskal-Wallis test, p < 0.01), but all vaginal samples had a similar diversity. The PERMANOVA analyses revealed significant differences (p < 0.01) between the microbial communities' structures from G and P sows. The bacteria phyla with the highest relative abundances were Proteobacteria (33.1%), followed by Firmicutes (32%), Cyanobacteria (13.3%) and Actinobacteria (13.2%). The relative abundance for phyla, families and genera was estimated and Proteobacteria was significantly higher (p = 0.038) in P than in G sows; Firmicutes was significantly lower in AI than G and NM sows. A "core microbiota" included Lactobacillus, Bacillus, Enterococcus, Acinetobacter and Pseudomonas. The results presented highlight the differences in the bacterial composition between G and P sows, as well as the changes in the microbial populations associated with the breeding method.